You should take a look at MLE+. It's a toolbox wich make the connection between Matlab and EnergyPlus. Obviously, you need to know the basics of EnergyPlus first.
By the way, if you're not very familiar with Matlab, why don't you go with TRNSYS or modelica. There are many other good programs to simulate energy transfert related with building engineering stuff.
I don't know what's your expectation but I you want to simulate something big and accurate, it's the way to go.